[gmx-users] drug-drug interaction energy

[Manuel Azenha]

Thanks for all your considerations on this subject!
I guess I must review the some of the underlying concepts.

Regards,

Manel

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
Justin Lemkul
Sent: 2 de abril de 2014 21:23
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] drug-drug interaction energy



On 4/2/14, 12:23 PM, Manuel Azenha wrote:
> Dear all,
>
>
>
> When I simulate a solution of a drug in water/methanol to study the 
> self-aggregation, and try to determine the interaction energy between 
> the drug molecules , I'm getting net positive values whatever the 
> drug. I'm simply defining the drug groups in .mdp. Should it be 
> entered some other way ?

How do those energies compare to the drug-water or drug-methanol energies? 
Remember that a pairwise nonbonded interaction energy is not a free energy.
If you used PME, the value returned by energygrps isn't even fully accurate
because the mesh term is not decomposed.  The magnitude of the effect
probably depends on the size of the molecules being considered and the
distance over which they interact.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-request at gromacs.org.